[CHNOSZ-commits] r186 - in pkg/CHNOSZ: . R data inst

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Mar 20 13:46:58 CET 2017 

Author: jedick
Date: 2017-03-20 13:46:58 +0100 (Mon, 20 Mar 2017)
New Revision: 186

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.data.R
   pkg/CHNOSZ/data/refs.csv
   pkg/CHNOSZ/inst/NEWS
Log:
some fixes for data/refs.csv


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-03-17 11:54:22 UTC (rev 185)
+++ pkg/CHNOSZ/DESCRIPTION	2017-03-20 12:46:58 UTC (rev 186)
@@ -1,6 +1,6 @@
-Date: 2017-03-17
+Date: 2017-03-20
 Package: CHNOSZ
-Version: 1.0.8-74
+Version: 1.0.8-75
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R	2017-03-17 11:54:22 UTC (rev 185)
+++ pkg/CHNOSZ/R/util.data.R	2017-03-20 12:46:58 UTC (rev 186)
@@ -197,7 +197,7 @@
     # append the counts to the table to be shown
     x <- c(list(number=number), x)
     # title to display for web page
-    title <- "Sources of Thermodynamic Data in CHNOSZ"
+    title <- "References for thermodynamic data in CHNOSZ"
     ### the following is adapted from print.findFn in package 'sos'
     f0 <- tempfile()
     File <- paste(f0, ".html", sep="")
@@ -259,10 +259,10 @@
     .cat("</head>")
     ### boilerplate text
     .cat("<body>")
-    .cat("<h1>Listing of all entries in thermo$refs</h1>")
-    .cat("<h3>Click on hyperlinked references to open URL in new window.</h3>")
-    .cat("<h3>Click on column headers to sort.</h3>")
-    .cat("<h3>Column 'number' gives number of times each reference appears in thermo$obigt.</h3>")
+    .cat('<h1>References for thermodynamic data in <a href="http://chnosz.net"><font color="red">CHNOSZ</font></a></h1>')
+    .cat("<h3>Click on a column header to sort, or on a citation to open the URL in new window.</h3>")
+    .cat("<h4>Column 'number' gives the number of times each reference appears in thermo$obigt.</h4>")
+    .cat('<p>See also the vignette <a href="http://chnosz.net/vignettes/obigt.html">Thermodynamic data in CHNOSZ</a>.</p>')
     ### start table and headers
     .cat("<table id='thermorefs' border='1'>")
     .cat("<tr>")

Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv	2017-03-17 11:54:22 UTC (rev 185)
+++ pkg/CHNOSZ/data/refs.csv	2017-03-20 12:46:58 UTC (rev 186)
@@ -11,9 +11,9 @@
 RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452","dickite, fluorphlogopite, halloysite, and pyrope",http://pubs.er.usgs.gov/publication/b1452
 RHF79.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452",iron,http://pubs.er.usgs.gov/publication/b1452
 PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",http://dx.doi.org/10.1016/0016-7037(82)90056-4
-WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392","gases GHS",http://dx.doi.org/10.1063/1.555661
-WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",manganosite,http://dx.doi.org/10.1063/1.555661
-WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",MgSO<sub>4</sub>,http://dx.doi.org/10.1063/1.555661
+WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
+WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",manganosite,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
+WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392",MgSO<sub>4</sub>,https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
 BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,http://dx.doi.org/10.1016/0016-7037(83)90066-2
 Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",http://dx.doi.org/10.2475/ajs.285.9.845
 JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",http://dx.doi.org/10.2113/gsecongeo.80.5.1365
@@ -64,8 +64,8 @@
 PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",http://dx.doi.org/10.1016/S0016-7037(99)00146-5
 SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479","jarosite, natroalunite, and natrojarosite",http://dx.doi.org/10.2138/rmg.2000.40.9
 AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,http://dx.doi.org/10.1016/S0016-7037(01)00707-4
-AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","NO and N<sub>2</sub>O",http://dx.doi.org/10.1016/S0168-6445(00)00062-0
-AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",http://dx.doi.org/10.1016/S0168-6445(00)00062-0
+AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","NO and N<sub>2</sub>O",http://dx.doi.org/10.1111/j.1574-6976.2001.tb00576.x
+AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",http://dx.doi.org/10.1111/j.1574-6976.2001.tb00576.x
 MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","ice polymorphs",http://dx.doi.org/10.1016/S0883-2927(00)00025-1
 PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes",http://dx.doi.org/10.1016/S0016-7037(01)00678-0
 Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",http://dx.doi.org/10.1016/S0016-7037(01)00761-X
@@ -74,7 +74,7 @@
 MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"Am. Mineral. 88, 846-854","goethite, lepidocrocite, and maghemite Cp",http://dx.doi.org/10.2138/am-2003-5-613
 MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531","hydronium jarosite",http://dx.doi.org/10.1007/s00269-004-0405-z
 SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097","alkane thiols",http://dx.doi.org/10.1016/j.gca.2003.06.001
-HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",http://dx.doi.org.ezproxy1.lib.asu.edu/10.1016/j.jct.2005.10.013
+HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007","methyldiethanolamine and methyldiethanolammonium chloride HKF parameters",http://dx.doi.org/10.1016/j.jct.2005.10.013
 LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","nucleic-acid bases, nucleosides, and nucleotides",http://dx.doi.org/10.1016/j.gca.2006.04.010
 LH06a.1,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724","citric acid and citrate",http://dx.doi.org/10.1016/j.gca.2006.04.010
 LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106","Mg-complexed adenosine nucleotides (ATP), NAD, and NADP",http://dx.doi.org/10.1016/j.tca.2006.06.008
@@ -94,10 +94,10 @@
 MA10,"L. Marini and M. Accornero",2010,"Environ. Earth Sci. 59, 1601-1606","corrected values",http://dx.doi.org/10.1007/s12665-009-0369-x
 Sch10,"M. Schulte",2010,"Aquat. Geochem. 16, 621-637","organic sulfides",http://dx.doi.org/10.1007/s10498-010-9102-3
 RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350","organic iodine compounds",http://dx.doi.org/10.1016/j.gca.2011.07.030
-LD12,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins",http://10.1016/j.gca.2011.11.041
-LD12.1,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","updated and corrected parameters for cysteine, glycine, leucine, and methionine",http://10.1016/j.gca.2011.11.041
-LD12.2,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine GHS",http://10.1016/j.gca.2011.11.041
-LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",http://10.1016/j.gca.2011.11.041
+LD12,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins",http://dx.doi.org/10.1016/j.gca.2011.11.041
+LD12.1,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","updated and corrected parameters for cysteine, glycine, leucine, and methionine",http://dx.doi.org/10.1016/j.gca.2011.11.041
+LD12.2,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine GHS",http://dx.doi.org/10.1016/j.gca.2011.11.041
+LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",http://dx.doi.org/10.1016/j.gca.2011.11.041
 DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"Geochim. Cosmochim. Acta 122, 247-266","phenanthrene and methylphenanthrene isomers",http://dx.doi.org/10.1016/j.gca.2013.08.020
 SLOP15.1,"E. L. Shock et al.",2015,"slop15.dat computer data file",""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."",http://geopig.asu.edu/?q=tools
 SLOP15.2,"E. L. Shock et al.",2015,"slop15.dat computer data file","Zn(Ac)3-: "Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."",http://geopig.asu.edu/?q=tools

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-03-17 11:54:22 UTC (rev 185)
+++ pkg/CHNOSZ/inst/NEWS	2017-03-20 12:46:58 UTC (rev 186)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-74 (2017-03-17)
+CHANGES IN CHNOSZ 1.0.8-75 (2017-03-20)
 ---------------------------------------
 
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